Chloranthus genome provides insights into the early diversification of angiosperms

Chloranthales remain the last major mesangiosperm lineage without a nuclear genome assembly. We therefore assemble a high-quality chromosome-level genome of Chloranthus spicatus to resolve enigmatic evolutionary relationships, as well as explore patterns of genome evolution among the major lineages of mesangiosperms (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales). We find that synteny is highly conserved between genomic regions of Amborella, Vitis, and Chloranthus. We identify an ancient single whole-genome duplication (WGD) (κ) prior to the divergence of extant Chloranthales. Phylogenetic inference shows Chloranthales as sister to magnoliids. Furthermore, our analyses indicate that ancient hybridization may account for the incongruent phylogenetic placement of Chloranthales + magnoliids relative to monocots and eudicots in nuclear and chloroplast trees. Long genes and long introns are found to be prevalent in both Chloranthales and magnoliids compared to other angiosperms. Overall, our findings provide an improved context for understanding mesangiosperm relationships and evolution and contribute a valuable genomic resource for future investigations.

Whole-genome sequencing analysis reveals the population history of Mus musculus in Madagascar

In Madagascar, the house mouse (Mus musculus) is thought to have colonized along with humans and is now one of the most successfully colonized rodents on the island. In this study, we determined the whole-genome sequences of the Madagascar house mouse captured from the wild. We examined the evolutionary history of its population regarding the mitochondrial and autosomal genomes. We confirmed that in the mitochondrial genomes of Madagascar house mice, a monophyletic clade forms a basal origin within the species. An analysis of autosomal genomic sequences indicates that the Madagascar house mouse population is genetically a member of M. m. castaneus (CAS). It also contains genetic elements of M. m. domesticus (DOM) resulting from ancient hybridization. The signature of a strong population bottleneck 1000–3000 years ago was observed in the mitochondrial and autosomal genomic data. We also show that the divergence of the Madagascar population from the CAS population occurred approximately 50,000–99,000 years ago. Madagascar house mice show strong genetic affinity to many CAS samples across a wide range of Indian Ocean coastal regions. However, our results suggest that they would not have originated directly from the Indonesian islands, where Austronesian-speaking people in Madagascar originated. Because the ancient hybridization signature with DOM did not appear in the Indonesian and other CAS samples, we propose that Madagascar house mice were not directly brought by Austronesian-speaking people but came from somewhere around the Middle East or South Asia soon after the colonization of initial farmers.

Integrated Genomic Analyses From Low-Depth Sequencing Help Resolve Phylogenetic Incongruence in the Bamboos (Poaceae: Bambusoideae)

The bamboos (Bambusoideae, Poaceae) comprise a major grass lineage with a complex evolutionary history involving ancient hybridization and allopolyploidy. About 1700 described species are classified into three tribes, Olyreae (herbaceous bamboos), Bambuseae (tropical woody bamboos), and Arundinarieae (temperate woody bamboos). Nuclear analyses strongly support monophyly of the woody tribes, whereas plastome analyses strongly support paraphyly, with Bambuseae sister to Olyreae. Our objectives were to clarify the origin(s) of the woody bamboo tribes and resolve the nuclear vs. plastid conflict using genomic tools. For the first time, plastid and nuclear genomic information from the same bamboo species were combined in a single study. We sampled 51 species of bamboos representing the three tribes, estimated their genome sizes and generated low-depth sample sequence data, from which plastomes were assembled and nuclear repeats were analyzed. The distribution of repeat families was found to agree with nuclear gene phylogenies, but also provides novel insights into nuclear evolutionary history. We infer two early, independent hybridization events, one between an Olyreae ancestor and a woody ancestor giving rise to the two Bambuseae lineages, and another between two woody ancestors giving rise to the Arundinarieae. Retention of the Olyreae plastome associated with differential dominance of nuclear genomes and subsequent diploidization in some lineages explains the paraphyly observed in plastome phylogenetic estimations. We confirm ancient hybridization and allopolyploidy in the origins of the extant woody bamboo lineages and propose biased fractionation and diploidization as important factors in their evolution.

Evolution of gene-rich germline restricted chromosomes in black-winged fungus gnats through introgression (Diptera: Sciaridae)

Germline restricted DNA has evolved in diverse animal taxa, and is found in several vertebrate clades, nematodes, and flies. In these lineages, either portions of chromosomes or entire chromosomes are eliminated from somatic cells early in development, restricting portions of the genome to the germline. Little is known about why germline restricted DNA has evolved, especially in flies, in which three diverse families, Chironomidae, Cecidomyiidae, and Sciaridae exhibit germline restricted chromosomes (GRCs). We conducted a genomic analysis of germline restricted chromosomes in the fungus gnat Bradysia (Sciara) coprophila (Diptera: Sciaridae), which carries two large germline restricted “L” chromosomes. We sequenced and assembled the genome of B. coprophila, and used differences in sequence coverage and k-mer frequency between somatic and germ tissues to identify GRC sequence and compare it to the other chromosomes in the genome. We found that the GRCs in B. coprophila are large, gene-rich, and have many genes with paralogs on other chromosomes in the genome. We also found that the GRC genes are extraordinarily divergent from their paralogs, and have sequence similarity to another Dipteran family (Cecidomyiidae) in phylogenetic analyses, suggesting that these chromosomes have arisen in Sciaridae through introgression from a related lineage. These results suggest that the GRCs may have evolved through an ancient hybridization event, raising questions about how this may have occurred, how these chromosomes became restricted to the germline after introgression, and why they were retained over time.

A synopsis of Phragmites (Poaceae) for Belarus

A taxonomic review of the Phragmites Adans. (Poaceae) in Belarus is presented. It is shown that P. nigricans (Mérat) Val. N. Tikhom. is the priority name of the widespread species formerly known as P. communis Trin. The new species P. tzvelevii Val. N. Tikhom. is described, which is apparently the result of ancient hybridization of P. nigricans and P. altissimus (Benth.) Mabille. The lectotype of the name P. nigricans is designated. A key for identification and brief descriptions of five Phragmites species identified in Belarus are provided.

The bear bones: mosaic ancestry of Macaca arctoides explains divergent baculum morphology

Genital divergence contributes to reproductive barriers between species. Emergence of a novel accessory structure, the baculum, has independently evolved and been lost throughout mammalian evolution, purportedly driven by sexual selection. In primates, the longest recorded baculum belongs to Macaca arctoides, the bear macaque. This species has been proposed to be of homoploid hybrid origin via ancient hybridization between representatives from the fascicularis and sinica species groups. To investigate the evolutionary origins of the bear macaque and its unique morphology, we used whole genome sequences to quantify gene flow and phylogenetic relationships in 10 individuals from 5 species, including the bear macaque (n=3), and two species each from the sinica (n=3) and fascicularis (n=4) species groups. The results of these analyses were concordant, and identified 608 genes in the bear macaque that supported both clustering between M. arctoides and the sinica group (topo2) and had shared derived alleles between species from the two groups. Similarly, 361 genes supported both clustering between M. arctoides and the fascicularis group (topo3) and had shared derived alleles between both groups. Further, sliding window analysis of phylogenetic relationships revealed 53% of the genomic regions supported placement of M. arctoides in the sinica species group (topo2), 16% supported placement in the fascicularis species group (topo3), and 11% supported M. arctoides in a grouping distinct from the sinica and fascicularis groups (topo1). Genomic regions with topo1 were intersected with previously identified QTL for mouse baculum morphology, and 47 genes were found, including five of sixteen major candidate loci that govern mouse baculum variation (KIF14, KIAA0586, RHOJ, TGM2, and DACT1). Although baculum morphology in the bear macaque is diverged from its parent taxa, it most closely resembles that of the fascicularis group. Outliers of shared ancestry from the fascicularis species group located within these same QTL regions overlap with the gene BMP4, which is an important component of the hedgehog signaling pathway that controls gonadogenesis. Two additional outlier genes (one shared with each species group) outside of the baculum QTL are known to interact with BMP4, suggesting this pathway may be involved in baculum morphology in primates. These results highlight how the mosaic ancestry of the bear macaque could explain its unique baculum evolution and collectively contribute to reproductive isolation.Introductory ParagraphIn mammals, the baculum has extreme morphological variability, a dynamic evolutionary history characterized by repeated gain and loss, and is often used in species identification. The bear macaque has divergent genital morphology, including the longest baculum among all primates, and is proposed to have evolved via ancient hybrid speciation. Here, population genetic and phylogenomic approaches were used to examine how ancient hybridization in the bear macaque may have shaped this important component of genital morphology. Results demonstrate extensive mosaicism across the genome, which is consistent with ancient genetic contributions from both putative parental taxa. Genetic regions associated with baculum morphology also had mosaic ancestry for several genes, including KIF14 and KIAA0586, major candidate genes for baculum morphology in mice, and BMP4, a developmental gene involved in gonadogenesis. These results have important implications for how hybridization may have shaped the evolution of reproductive isolation in this unusual species with complex speciation.